
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
import shutil
import os
from tempfile import TemporaryDirectory

use_tempdir = True
if use_tempdir:
    # Create temporary directory
    data_dir = TemporaryDirectory()
    # Save original directory
    orig_dir = os.getcwd()
    # Move to new directory
    os.chdir(data_dir.name)

# For info, print out where the script is running
print("Running in {}".format(os.getcwd()))

Running in /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.pipeline.calwebb_spec2 import Spec2Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
    from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
    from jwst.extract_2d.extract_2d_step import Extract2dStep
    from jwst.srctype.srctype_step import SourceTypeStep
    from jwst.wavecorr.wavecorr_step import WavecorrStep
    from jwst.flatfield.flat_field_step import FlatFieldStep

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Print versions used for the pipeline and NPTT

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.7.2
Using NPTT version:  2.0.1


testing_data = {

                'ifu_g395h_f290lp':{
                                  'uncal_file_nrs1': 'ifu_g395h_f290lp_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'ifu_g395h_f290lp_nrs2_uncal.fits',
                                  'sflat_nrs1': 'nirspec_IFU_sflat_G395H_OPAQUE_FLAT3_nrs1_f_01.01.fits',
                                  'sflat_nrs2': 'nirspec_IFU_sflat_G395H_OPAQUE_FLAT3_nrs2_f_01.01.fits',
                                  'fflat': 'nirspec_IFU_fflat_F290LP_01.01.fits',
                                  'msa_shutter_config': None }

                }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'sflat_nrs1', 'fflat', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# set the D-flat path (used for all test data)
print('Getting D-Flats from Artifactory...')

dflat_nrs1 = get_bigdata('jwst_validation_notebooks',
                         'validation_data',
                         'nirspec_data', 
                         'nirspec_dflat_nrs1_f_01.03.fits')

dflat_nrs2 = get_bigdata('jwst_validation_notebooks',
                         'validation_data',
                         'nirspec_data', 
                         'nirspec_dflat_nrs2_f_01.03.fits')
print('Got D-flats')

# set NPTT switches for this test and other variables
writefile = False
save_figs = False
show_figs = True
results_dict = {}
detectors = ['nrs1', 'nrs2']

Getting D-Flats from Artifactory...
Got D-flats


# Get data for IFU

for mode_config, data_set_dict in testing_data.items():
    if 'ifu' not in mode_config:
        continue
        
    print('Starting to run pipeline and test for mode: ', mode_config)
    
    for detector in detectors:
        print('Testing files for detector: ', detector)
        data = get_artifactory_file(data_set_dict, detector)
        uncal_file, sflat, fflat, msa_shutter_config = data
        print('Working with uncal_file: ', uncal_file)
        uncal_basename = os.path.basename(uncal_file)
        dflat = dflat_nrs1
        if '2' in detector:
            dflat = dflat_nrs2
        
        # Make sure these keywords are properly set
        filt = fits.getval(uncal_file, 'FILTER')
        if 'OPAQUE' in filt or 'allslits' in uncal_basename.lower():
            if 'clear' in uncal_basename.lower():
                filt = 'CLEAR'
            else:
                l = uncal_basename.split("_")
                for li in l:
                    if 'lp' in li.lower():
                        filt = li
                        break
            fits.setval(uncal_file, 'FILTER', value=filt)
        print('Filter = ', filt)

        # Run the stage 1 pipeline 
        print('Running the detector1 pipeline...')
        rate_object = Detector1Pipeline.call(uncal_file)
        
        # Make sure the FXD_SLIT keyword is set correctly
        try:
            if 'full' in rate_object.meta.instrument.fixed_slit:
                rate_object.meta.instrument.fixed_slit = 'NONE'
        except TypeError:
            print('FXD_SLIT keyword = ', rate_object.meta.instrument.fixed_slit)
        
        # Run the stage 2 pipeline steps
        print('\nRunning the spec2 pipeline...')
        skip_file = False
        try:
            parameter_dict = {"flat_field": {"save_interpolated_flat": True},
                              "pathloss": {"skip": True},
                              "barshadow": {"skip": True},
                              "photom": {"skip": True},
                              "resample_spec": {"skip": True},
                              "cube_build": {"skip": True},
                              "extract_1d": {"skip": True}
                             }
            flat_field_object = Spec2Pipeline.call(rate_object, steps=parameter_dict)
        except:
            #print("No open slits fall on detector ", det)  # usually why assign_wcs crashes
            print("* Spec2 pipeline CRASHED or exited with no output for detector ", detector)
            print("  Skipping test for this file. \n")
            skip_file = True
            
        if not skip_file:   
            # accepted threshold difference with respect to benchmark files
            threshold_diff = 9.999e-5
            if 'prism' in uncal_basename.lower():
                threshold_diff = 9.999e-3
            
            # Run the validation test
            %matplotlib inline
            interpolated_flat = os.path.basename(uncal_file).replace('uncal', 'interpolatedflat')
            print('Running flat field test for IFU...')
            result, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.flattest_ifu.flattest(
                                                                            flat_field_object,
                                                                            dflat_path=dflat,
                                                                            sflat_path=sflat, 
                                                                            fflat_path=fflat,
                                                                            writefile=writefile,
                                                                            mk_all_slices_plt=False, 
                                                                            show_figs=show_figs, 
                                                                            save_figs=save_figs,
                                                                            interpolated_flat=interpolated_flat,
                                                                            threshold_diff=threshold_diff,
                                                                            debug=False)
        else:
            result, result_msg = 'skipped', 'skipped'

        # Did the test passed 
        print("Did flat_field for ", mode_config, " validation test passed? ", result_msg, "\n\n")
        rd = {uncal_basename: result}
        results_dict.update(rd)
        
        # close all open files
        psutil.Process().open_files()
        closing_files = []
        for fd in psutil.Process().open_files():
            if data_dir.name in fd.path:
                closing_files.append(fd)
        for fd in closing_files:
            try:
                print('Closing file: ', fd, '\n\n')
                open(fd.fd).close()
            except:
                print('File already closed: ', fd, '\n\n')

Starting to run pipeline and test for mode:  ifu_g395h_f290lp
Testing files for detector:  nrs1
Working with uncal_file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5/ifu_g395h_f290lp_nrs1_uncal.fits
Filter =  F290LP
Running the detector1 pipeline...

2022-10-05 22:03:26,644 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-10-05 22:03:26,669 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-10-05 22:03:26,670 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-10-05 22:03:26,672 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-10-05 22:03:26,673 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-10-05 22:03:26,674 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-10-05 22:03:26,675 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-10-05 22:03:26,676 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-10-05 22:03:26,677 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-10-05 22:03:26,678 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-10-05 22:03:26,679 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-10-05 22:03:26,680 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-10-05 22:03:26,681 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-10-05 22:03:26,683 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-10-05 22:03:26,684 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-10-05 22:03:26,685 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-10-05 22:03:26,686 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-10-05 22:03:26,687 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-10-05 22:03:26,806 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5/ifu_g395h_f290lp_nrs1_uncal.fits',).
2022-10-05 22:03:26,816 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-10-05 22:03:27,206 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-10-05 22:03:27,222 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits'.
2022-10-05 22:03:27,223 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits'.
2022-10-05 22:03:27,225 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits'.
2022-10-05 22:03:27,227 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2022-10-05 22:03:27,229 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-10-05 22:03:27,229 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2022-10-05 22:03:27,231 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits'.
2022-10-05 22:03:27,232 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-10-05 22:03:27,232 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-10-05 22:03:27,233 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits'.
2022-10-05 22:03:27,234 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits'.
2022-10-05 22:03:27,236 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-10-05 22:03:27,236 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-10-05 22:03:27,237 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-10-05 22:03:28,092 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:28,093 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:03:28,602 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-10-05 22:03:28,603 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-10-05 22:03:28,605 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-10-05 22:03:28,725 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:28,727 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:03:28,749 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2022-10-05 22:03:30,040 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-10-05 22:03:30,203 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:30,205 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5', 'n_pix_grow_sat': 1}
2022-10-05 22:03:30,230 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0027.fits
2022-10-05 22:03:35,409 - stpipe.Detector1Pipeline.saturation - INFO - Detected 218077 saturated pixels
2022-10-05 22:03:35,555 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-10-05 22:03:35,582 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-10-05 22:03:35,705 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:35,707 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:03:35,707 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-10-05 22:03:35,710 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-10-05 22:03:35,819 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:35,820 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:03:35,844 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:38: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']

Failed validating 'enum' in schema:
    OrderedDict([('title', 'Readout pattern'),
                 ('type', 'string'),
                 ('enum',
                  ['ACQ1',
                   'ACQ2',
                   'BRIGHT1',
                   'BRIGHT2',
                   'DEEP2',
                   'DEEP8',
                   'FAST',
                   'FASTGRPAVG',
                   'FASTGRPAVG8',
                   'FASTGRPAVG16',
                   'FASTGRPAVG32',
                   'FASTGRPAVG64',
                   'FASTR1',
                   'FASTR100',
                   'FGS',
                   'FGS60',
                   'FGS8370',
                   'FGS840',
                   'FGSRAPID',
                   'FINEGUIDE',
                   'ID',
                   'MEDIUM2',
                   'MEDIUM8',
                   'NIS',
                   'NISRAPID',
                   'NRS',
                   'NRSIRS2',
                   'NRSN16R4',
                   'NRSN32R8',
                   'NRSN8R2',
                   'NRSRAPID',
                   'NRSIRS2RAPID',
                   'NRSRAPIDD1',
                   'NRSRAPIDD2',
                   'NRSRAPIDD6',
                   'NRSSLOW',
                   'RAPID',
                   'SHALLOW2',
                   'SHALLOW4',
                   'SLOW',
                   'SLOWR1',
                   'TRACK',
                   'ANY',
                   'N/A']),
                 ('fits_ke ...
  warnings.warn(errmsg, ValidationWarning)
2022-10-05 22:03:38,428 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-10-05 22:03:38,550 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:03:38,552 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-10-05 22:03:38,575 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits
2022-10-05 22:03:40,443 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1
2022-10-05 22:04:55,533 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-10-05 22:04:55,779 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:04:55,781 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:04:55,812 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits
2022-10-05 22:04:56,616 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2022-10-05 22:04:58,358 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-10-05 22:04:58,484 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:04:58,485 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5', 'dark_output': None}
2022-10-05 22:04:58,792 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits
2022-10-05 22:05:28,921 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2022-10-05 22:05:28,922 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2022-10-05 22:05:30,488 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-10-05 22:05:30,711 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:05:30,713 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0}
2022-10-05 22:05:30,861 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-10-05 22:05:31,027 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2022-10-05 22:05:31,569 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-10-05 22:05:32,570 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-10-05 22:05:32,735 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-10-05 22:05:40,394 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 64946 pixels with at least one CR from five or more groups.
2022-10-05 22:05:40,396 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 442 pixels with at least one CR from four groups.
2022-10-05 22:05:40,396 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 437 pixels with at least one CR from three groups.
2022-10-05 22:05:59,441 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 26.8695 sec
2022-10-05 22:05:59,448 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 28.587135
2022-10-05 22:05:59,454 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-10-05 22:05:59,726 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:05:59,728 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-10-05 22:06:00,110 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-10-05 22:06:00,111 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2022-10-05 22:06:00,210 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-10-05 22:06:00,211 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-10-05 22:08:51,229 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2022-10-05 22:08:51,230 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-10-05 22:08:51,439 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-10-05 22:08:51,622 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:08:51,624 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:08:51,686 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2022-10-05 22:08:51,703 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-10-05 22:08:51,815 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:08:51,816 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5'}
2022-10-05 22:08:51,880 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2022-10-05 22:08:51,898 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-10-05 22:08:51,898 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-10-05 22:08:51,899 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_0988.pmap
2022-10-05 22:08:51,899 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-10-05 22:08:51,944 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2022-10-05 22:08:51,945 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2022-10-05 22:08:51,946 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2022-10-05 22:08:51,947 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2022-10-05 22:08:51,948 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2022-10-05 22:08:51,950 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2022-10-05 22:08:51,953 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2022-10-05 22:08:51,954 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2022-10-05 22:08:51,955 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2022-10-05 22:08:51,956 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2022-10-05 22:08:51,957 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2022-10-05 22:08:51,958 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2022-10-05 22:08:51,959 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2022-10-05 22:08:51,960 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2022-10-05 22:08:51,962 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2022-10-05 22:08:51,963 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2022-10-05 22:08:51,964 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2022-10-05 22:08:51,965 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2022-10-05 22:08:51,966 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2022-10-05 22:08:51,968 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2022-10-05 22:08:51,970 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2022-10-05 22:08:51,971 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2022-10-05 22:08:51,972 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2022-10-05 22:08:52,086 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:08:52,100 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_bsub': False, 'fail_on_exception': True, 'save_wfss_esec': False, 'steps': {'bkg_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}, 'assign_wcs': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}, 'imprint_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'msa_flagging': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'extract_2d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}, 'master_background_mos': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'force_subtract': False, 'save_background': False, 'user_background': None, 'inverse': False, 'steps': {'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}}}, 'wavecorr': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': True, 'user_supplied_flat': None, 'inverse': False}, 'srctype': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}, 'straylight': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'fringe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'wfss_contam': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_simulated_image': False, 'save_contam_images': False, 'maximum_cores': 'none'}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'resample_spec': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'weight_type': 'ivm', 'output_shape': None, 'crpix': None, 'crval': None, 'rotation': None, 'pixel_scale_ratio': 1.0, 'pixel_scale': None, 'single': False, 'blendheaders': True, 'allowed_memory': None, 'in_memory': True}, 'cube_build': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'band', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'drizzle', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 2.0, 'wavemin': None, 'wavemax': None, 'single': False, 'skip_dqflagging': False}, 'extract_1d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'smoothing_length': None, 'bkg_fit': None, 'bkg_order': None, 'bkg_sigma_clip': 3.0, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'center_xy': None, 'apply_apcorr': True, 'soss_threshold': 0.01, 'soss_n_os': 2, 'soss_transform': None, 'soss_tikfac': None, 'soss_width': 40.0, 'soss_bad_pix': 'model', 'soss_modelname': None}}}
2022-10-05 22:08:52,110 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs1_uncal.fits' reftypes = ['camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']

Running the spec2 pipeline...

2022-10-05 22:08:52,131 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf'.
2022-10-05 22:08:52,132 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf'.
2022-10-05 22:08:52,134 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dflat_0001.fits'.
2022-10-05 22:08:52,135 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf'.
2022-10-05 22:08:52,137 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2022-10-05 22:08:52,138 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fflat_0010.fits'.
2022-10-05 22:08:52,139 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2022-10-05 22:08:52,140 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2022-10-05 22:08:52,140 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf'.
2022-10-05 22:08:52,141 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf'.
2022-10-05 22:08:52,144 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2022-10-05 22:08:52,144 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf'.
2022-10-05 22:08:52,146 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf'.
2022-10-05 22:08:52,147 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'.
2022-10-05 22:08:52,148 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2022-10-05 22:08:52,149 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf'.
2022-10-05 22:08:52,151 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json'.
2022-10-05 22:08:52,152 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf'.
2022-10-05 22:08:52,155 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2022-10-05 22:08:52,155 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_sflat_0015.fits'.
2022-10-05 22:08:52,156 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2022-10-05 22:08:52,157 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2022-10-05 22:08:52,157 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0005.asdf'.
2022-10-05 22:08:52,158 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2022-10-05 22:08:52,159 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2022-10-05 22:08:52,217 - stpipe.Spec2Pipeline - INFO - Processing product ifu_g395h_f290lp_nrs1_uncal
2022-10-05 22:08:52,218 - stpipe.Spec2Pipeline - INFO - Working on input <IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits> ...
2022-10-05 22:08:52,340 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:08:52,341 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.25, 'sip_degree': None, 'sip_max_inv_pix_error': 0.25, 'sip_inv_degree': None, 'sip_npoints': 32, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2022-10-05 22:08:52,546 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1448970586061478 deg
2022-10-05 22:08:52,547 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3232757747173309 deg
2022-10-05 22:08:52,548 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: -3.766823889842878e-13 deg
2022-10-05 22:08:52,549 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0 deg
2022-10-05 22:08:56,024 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0005.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
2022-10-05 22:09:04,102 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS  156.176999392 -45.687618156 156.178775679 -45.687618156 156.178775679 -45.686331563 156.176999392 -45.686331563
2022-10-05 22:09:04,105 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2022-10-05 22:09:04,119 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2022-10-05 22:09:04,432 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>, []).
2022-10-05 22:09:04,433 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}
2022-10-05 22:09:04,434 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2022-10-05 22:09:04,436 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2022-10-05 22:09:04,619 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>, []).
2022-10-05 22:09:04,620 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-10-05 22:09:04,621 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2022-10-05 22:09:04,624 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract done
2022-10-05 22:09:04,806 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:09:04,808 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-10-05 22:09:04,829 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2022-10-05 22:09:04,831 - stpipe.JwstStep - INFO - JwstStep instance created.
2022-10-05 22:09:05,013 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.1448970586061478 deg
2022-10-05 22:09:05,014 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.3232757747173309 deg
2022-10-05 22:09:05,015 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: -3.766823889842878e-13 deg
2022-10-05 22:09:05,016 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0 deg
2022-10-05 22:09:05,033 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2022-10-05 22:09:05,228 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 5 open slits in quadrant 1
2022-10-05 22:09:05,279 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2022-10-05 22:09:05,306 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 9 open slits in quadrant 3
2022-10-05 22:09:05,384 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2022-10-05 22:09:05,411 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2525.1239286219193.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2239.8443211081017.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2382.5735098584228.
  warnings.warn(f"Invalid interval: upper bound {upper} "
2022-10-05 22:09:22,286 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2022-10-05 22:09:23,034 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:09:23,036 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}
2022-10-05 22:09:23,047 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_IFU
2022-10-05 22:09:23,048 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2022-10-05 22:09:23,048 - stpipe.Spec2Pipeline.srctype - INFO - Input source type is unknown; setting default SRCTYPE = EXTENDED
2022-10-05 22:09:23,051 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2022-10-05 22:09:23,404 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:09:23,406 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': True, 'user_supplied_flat': None, 'inverse': False}
2022-10-05 22:16:56,239 - stpipe.Spec2Pipeline.flat_field - INFO - Saved model in ifu_g395h_f290lp_nrs1_interpolatedflat.fits
2022-10-05 22:16:56,241 - stpipe.Spec2Pipeline.flat_field - INFO - Interpolated flat written to "ifu_g395h_f290lp_nrs1_interpolatedflat.fits".
2022-10-05 22:16:56,248 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2022-10-05 22:16:57,439 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:16:57,441 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-10-05 22:16:57,443 - stpipe.Spec2Pipeline.straylight - INFO - Step skipped.
2022-10-05 22:16:57,446 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2022-10-05 22:16:57,763 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:16:57,765 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-10-05 22:16:57,766 - stpipe.Spec2Pipeline.fringe - INFO - Step skipped.
2022-10-05 22:16:57,769 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2022-10-05 22:16:58,086 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:16:58,088 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-10-05 22:16:58,089 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2022-10-05 22:16:58,092 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2022-10-05 22:16:58,410 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:16:58,411 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-10-05 22:16:58,412 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2022-10-05 22:16:58,415 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2022-10-05 22:16:58,734 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-10-05 22:16:58,735 - stpipe.Spec2Pipeline.photom - INFO - Step photom parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-10-05 22:16:58,736 - stpipe.Spec2Pipeline.photom - INFO - Step skipped.
2022-10-05 22:16:58,739 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2022-10-05 22:16:59,091 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_cal.fits>,).
2022-10-05 22:16:59,093 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'multi', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'drizzle', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 2.0, 'wavemin': None, 'wavemax': None, 'single': False, 'skip_dqflagging': True}
2022-10-05 22:16:59,094 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2022-10-05 22:16:59,097 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2022-10-05 22:16:59,341 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_cal.fits>,).
2022-10-05 22:16:59,343 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 'x1d', 'search_output_file': True, 'input_dir': '', 'smoothing_length': None, 'bkg_fit': None, 'bkg_order': None, 'bkg_sigma_clip': 3.0, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'center_xy': None, 'apply_apcorr': True, 'soss_threshold': 0.01, 'soss_n_os': 2, 'soss_transform': None, 'soss_tikfac': None, 'soss_width': 40.0, 'soss_bad_pix': 'model', 'soss_modelname': None}
2022-10-05 22:16:59,344 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2022-10-05 22:16:59,346 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2022-10-05 22:16:59,347 - stpipe.Spec2Pipeline - INFO - Finished processing product ifu_g395h_f290lp_nrs1_uncal
2022-10-05 22:16:59,347 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2022-10-05 22:16:59,348 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_0988.pmap
2022-10-05 22:16:59,348 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done

Running flat field test for IFU...
flat_field_file  -->     Grating:G395H   Filter:F290LP   LAMP:REF
Getting and reading the D-, S-, and F-flats for this specific IFU configuration... 
Using D-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5/nirspec_dflat_nrs1_f_01.03.fits
Using S-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5/nirspec_IFU_sflat_G395H_OPAQUE_FLAT3_nrs1_f_01.01.fits
Using F-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp_31lz4w5/nirspec_IFU_fflat_F290LP_01.01.fits

 Now looping through the slices, this may take some time... 

Working with slice: 00
 Subwindow origin:   px0=275   py0=782
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 00

   Absolute Flat Difference  :   mean = 2.451e-07    median = 2.961e-07    stdev = 9.459e-05
    Maximum   AbsoluteFlat Difference = 6.543e-04
    Minimum   AbsoluteFlat Difference = -8.418e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 25%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...

 *** Result of the test: PASSED


Working with slice: 01
 Subwindow origin:   px0=312   py0=1198
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 01

   Absolute Flat Difference  :   mean = 6.821e-08    median = 2.047e-07    stdev = 1.043e-04
    Maximum   AbsoluteFlat Difference = 1.462e-03
    Minimum   AbsoluteFlat Difference = -9.074e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 29%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...

 *** Result of the test: PASSED


Working with slice: 02
 Subwindow origin:   px0=271   py0=732
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 02

   Absolute Flat Difference  :   mean = 9.632e-08    median = 4.646e-07    stdev = 9.722e-05
    Maximum   AbsoluteFlat Difference = 1.025e-03
    Minimum   AbsoluteFlat Difference = -8.078e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 26%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...

 *** Result of the test: PASSED


Working with slice: 03
 Subwindow origin:   px0=317   py0=1247
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 03

   Absolute Flat Difference  :   mean = -7.211e-09    median = 6.240e-07    stdev = 1.029e-04
    Maximum   AbsoluteFlat Difference = 7.566e-04
    Minimum   AbsoluteFlat Difference = -8.425e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 28%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...

 *** Result of the test: PASSED


Working with slice: 04
 Subwindow origin:   px0=266   py0=683
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 04

   Absolute Flat Difference  :   mean = 2.326e-07    median = 5.106e-07    stdev = 1.008e-04
    Maximum   AbsoluteFlat Difference = 7.220e-03
    Minimum   AbsoluteFlat Difference = -8.518e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 26%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...

 *** Result of the test: PASSED


Working with slice: 05
 Subwindow origin:   px0=321   py0=1297
 Looping through the wavelength, this may take a little time ... 
Flat value differences for slice number: 05

   Absolute Flat Difference  :   mean = -1.699e-07    median = 3.482e-07    stdev = 1.025e-04
    Maximum   AbsoluteFlat Difference = 9.310e-04
    Minimum   AbsoluteFlat Difference = -1.075e-03
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 28%
                            ->  3xtheshold = 1%
                            ->  5xtheshold = 0%
Making the plot for this slice...


# Quickly see if the test passed 

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<42} {:<8}'.format(key, val))

These are the final results of the tests: 
ifu_g395h_f290lp_nrs1_uncal.fits           PASSED  
ifu_g395h_f290lp_nrs2_uncal.fits           PASSED

JWST Pipeline Validation Testing Notebook: spec2, flat_field step¶

Table of Contents¶

Imports¶

Test Description¶

Test Results¶

Calibration WG Requested Algorithm:¶

Defining Term¶

Run the JWST pipeline and assign_wcs validation tests¶

Testing Data Set¶

About this Notebook¶